Friday, July 20, 2012

We Called Out IDiot Jonathan Wells, and He Folded

Carl Zimmer had the audacity to post something about the fusion of two ancestral chromosomes in primitive apes. The data is unequivocal. It shows why humans have one less chromosome than modern chimps [The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists)].

Observations like this lend strong support to the idea that humans and chimps share a common ancestor. This doesn't sit well with the IDiots because they are in the midst of hyping their latest book, Science & Human Origins where they try to counter the overwhelming evidence that humans evolved.

So, what did they do? David Klinghoffer challenged Carl Zimmer to pop on over to Evolution News & Views (sic) and debate one of the authors. Carl refused, as would any sane person since that creationist blog is edited by IDiots and no comments are allowed. It would be embarrassing to have one's name on an article at Evolution News & Views [The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger].

Here's what Carl said,
I thought the question I asked was pretty simple. I wasn’t asking to hold a Lincoln-Douglas debate. I just asked what the evidence was for one of the claims made by the creationists.

Now it seems that in order to get that answer, I can either buy a book–which apparently is based on no peer-reviewed research of the authors, but just cherry-picked quotes from a ten-year old paper–or I can donate my time to write several thousands words for free for a creationist web site.

Making this offer even richer is Klinghoffer’s ground rules about focusing “strictly on the ideas, not on the personalities.” Klinghoffer himself has used Evolution News & Views to call people pathetic, a worthless bully, cowards, illiterate, and “a tyranny of the unemployed” (referring to Wikipedia editors). In one piece he wrote for Evolution New and Views, Klinhoffer mocked a post by a science blogger as “preening and self-congratulatory.”

That blogger happened to be me.

I will answer Mr. Klinghoffer publicly: no thanks. I never asked for a debate, and your arbitrary decrees, such as a mysterious thousand-word cutoff (my blog post on the chromosomes alone clocked in at over 2,000 words) make it even less appealing. I am particularly opposed to web sites that do not allow readers to comment. That’s how I ended up on Facebook in the first place–because the Discovery Institute’s web sites do not permit commenting. You, on the other hand, are more than welcome to leave a comment on my blog. My comment policy is very lax: I only throw out commenters who curse uncontrollably, hawk their own wares, or can’t stay on topic after repeated warnings. We have a thriving, fascinating discussion here, one from which I regularly learn new things from my readers. You might too.
David Klinghoffer, being David Klinghoffer, responded with a blog posting on Evolution News & Views: We Called Out Darwinist Critic Carl Zimmer, and He Folded.

"Reasoning with a Lynch Mob"

This reminded me of an incident that took place last November. You might remember that I spent a great deal of time and effort reviewing Jonathan Wells' book, The Myth of Junk DNA (see The Myth of Junk DNA by Jonathan Wells). I invited Wells to discuss and debate the issue of junk DNA and my extensive criticism of his book.

Wells declined [Jonathan Wells Sends His Regrets]. Here's what he said ...
Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.
Sort of makes you wonder, doesn't it? Do you think the IDiots really are interested in debating science or is it only on their own terms, on their own blog, with no comments, and moderated by their own kind?


44 comments :

  1. Ideologues who demand debates and then cry "Coward!" when turned down remind of schoolyard toughs who try to pick fights, and then react the same way when ignored. Another example is William Lane Craig's "empty-chair" challenge to Dawkins a few months ago. It's just juvenile attention-seeking.

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  2. Wells is a member of the Mooney cult, that's something I didn't know. That means in addition to being an IDiot he's wants to make a the USA a theocracy under the Rev. Sun Myung Moon the Looney.

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  3. "David Klinghoffer, being David Klinghoffer, responded with a blog posting on Evolution News & Views:"

    Where, of course, comments aren't allowed.

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    1. Sometime it would be nice to query Mr. Klinghoffer, who purports to be an Orthodox Jew, as to why he associates himself with the Dishonesty Institute whose executive director, John West, is a sometime Holocaust revisionist.

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  4. The only difference between Wells and other crusaders against evolution, like Cornelius Hunter, is that, at one time, he was quite open about his motives"

    "Father's [Sun Myung Moon's] words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle." --Jonathan Wells, Darwinism: Why I Went for a Second Ph.D. [3]

    This is, of course, also the reason why I would not accept Wells's unsupported word about anything in science.

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  5. It's quite funny. I mentioned the chromosome 2 fusion in a previous thread and Joe Felsenstein folded. He didn't understand that the fusion serves as a reproductive barrier and that the mutation is highly unlikely to successfully diffuse and fix except in a very small population. It isn't like some neutral allele or the like.

    More generally, the chromosome 2 fusion does not indicate human-chimp ancestry because the first humans could have had 48 chromosomes and the fusion event might have been much more recent.

    Btw, I have suggested debating Larry in his backyard of Toronto about ID, junk DNA, Darwinism and other matters but he has so far not proven to be very responsive to an intellectual discourse where he has to answer some tough questions from a formidable opponent.

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    1. There is no evidence to suggest that the chromosome fusion was a reproductive barrier. In fact, all the data we have is consistent with it being a nearly neutral event.

      There are many species that harbor significant chromosomal rearrangements as natural variation.

      BTW, I'd be happy to debate any expert on junk DNA who disagrees with me. Do you know of one who wants to have a serious debate?

      I'd also be happy to debate Darwinism. As you know, I'm not a Darwinist. Do you know of an intelligent Darwinist who wants to defend the idea that "Darwinism" is the best description of modern evolutionary theory?

      As for Intelligent Design Creationism, I'd be interested in debating anyone who wants to present scientific evidence for the existence of an intelligent designer.

      ... he has so far not proven to be very responsive to an intellectual discourse where he has to answer some tough questions from a formidable opponent.

      How would you know? So far, I've never had to answer any tough questions from a formidable opponent so I've never had the privilege of an intellectual discourse with an IDiot.

      If you think you have any tough questions, please feel free to post them in the comments.

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    2. Larry, I suggest you learn the basics of reproductive isolation. The reason why a mule (the offspring of a horse with 64 chromosomes and donkey with 62) is infertile is because the chromosomes don't divide in a balanced way during meiosis. I do not know of any gorillas or chimps with similarly fused chromosomes (2a and 2b) that can interbreed successfully with wild-type members. Do you?

      I am aware that you claim to be a non-Darwinist and "pluralist", but that only means you endorse BOTH natural selection AND drift as equally valid and important mechanisms. I would be happy to debate you on Junk DNA given that my PhD dissertation focuses on understanding genomic organization and topology. There is a mountain of evidence I have painstakingly collated that I can throw at you.The genome is hardly a haphazard construction.

      I will admit, however, that you much more open and tolerant of opposing views, including from the IDiots, than the likes of PZ Myers and Jerry Coyne who are completely dismissive and who ban critics on their blog-sites.

      It is up to you, big guy. The Fall semester is not far away.

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    3. I would be happy to debate you on Junk DNA given that my PhD dissertation focuses on understanding genomic organization and topology. There is a mountain of evidence I have painstakingly collated that I can throw at you.The genome is hardly a haphazard construction.

      Okay, big guy, here's your chance.

      Prepare a brief article on why you think MOST pseudogenes and defective transposons are not junk and I'll put it up as a quest post.

      The one rule I insist on is that you specifically state what percentage of the genome is functional and what percentage is junk and defend those numbers. (I also expect you to post under your real name but that shouldn't be a problem.)

      P.S. Who is your Ph.D. supervisor? I'd like to make sure he/she will be following our discussion.

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    4. Atheistoclast says:

      "Larry, I suggest you learn the basics of reproductive isolation. The reason why a mule (the offspring of a horse with 64 chromosomes and donkey with 62) is infertile is because the chromosomes don't divide in a balanced way during meiosis. I do not know of any gorillas or chimps with similarly fused chromosomes (2a and 2b) that can interbreed successfully with wild-type members. Do you?"

      I know of a great ape that can successfully reproduce even with a fused chromosome. See http://en.wikipedia.org/wiki/Robertsonian_translocation. There's also the Przewalski's horse, which can successfully interbreed with domestic horses, despite different chromosome numbers. See http://en.wikipedia.org/wiki/Wild_horse.

      As a PhD candidate (if that's indeed what you are), you would do well to learn not to be so sure of the things you "know."

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    5. How many people with Down syndrome (caused by such translocations) do you know who can reproduce and have fertile offspring? Zebras and horses can interbreed, and have little zorses and hebras, but the chances of the offspring being able to reproduce are very low indeed.

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    6. Down syndrome is not caused by a translocation.

      The answer to the the reproduction and fertile offspring question is on Carl Zimmer's blog.

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    7. I think 'Atheistoclast' just spilled the beans - his claim to being a PhD student in a 'Genomics' department yet writes that trisomy 21 is the result of a translocation is clearly a fib.

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  6. There are cases of male and female primates, owl monkeys specifically, that have different karyotypes/chromosome numbers and have produced viable offpsring.

    Atheistoclast...can you tell me more about your dissertation research? Are you in a biology or computer science department?...or math? From what you wrote, it sounds like you are doing a dissertation showing that the genome is designed ("hardly a haphazard construction"). Do you mean designed by a creator/designer or designed by natural selection or designed by something else? I'm am intrigued by what you wrote...

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    1. I am now a PhD candidate in a Genomics department but specializing in computational bioinformatics. I am focusing on using AI techniques to understand the "layout" of the genome - how genes of different function are arranged, the distances between them, the location of those genes read antisense or sense, the variation in the GC content along the chromosome etc. It is quite apparent that genetic topology is distinctly non-random. Some genes may well get transposed and relocated, but the basic layout remains the same. The actual evolutionary mechanisms behind this topological arrangement are not my concern so much as and understanding of the nature of it and how it may affect gene expression.

      Btw, chromosomal variations per se do not represent reproductive barriers, but most experts agree that the chromosomal fusion in the human lineage was such a barrier (as it is in equids).

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    2. ... most experts agree that the chromosomal fusion in the human lineage was such a barrier

      No, they don't [Fusing Chromosomes]. The original fusion event could not have been (very) deleterious to the individual carrying it or they would never have been able to reproduce and the fusion chromosome would never have become fixed in the population.

      It may be rue that subsequent evolution and additional rearrangements has led to segregation incompatibility between chimps and humans. We don't know.

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    3. LOL, Larry. I hardly think an palaeo-anthropoligist is an expert on genetics. What chromosomal fusion does is to limit one's reproductive potential rather than to prevent it entirely. I suggest you read this paper that suggest that the fusion, along with several inversions, effectively make us reproductively isolate from the great apes:

      Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster.

      http://www.ncbi.nlm.nih.gov/sites/entrez/5636340?dopt=Abstract&holding=f1000,f1000m,isrctn

      Needless to say, speciation involves reproductive and/or geographical isolation.

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    4. I hardly think an palaeo-anthropoligist is an expert on genetics.

      John Hawks is one of the world's leading experts on population genetics as it applies to the evolution of humans. It's too bad you don't know this even after visiting his blog.

      I suggest you read this paper that suggest that the fusion, along with several inversions, effectively make us reproductively isolate from the great apes:

      Here's the correct link ...
      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC193642/?tool=pubmed

      I scanned the 2003 paper but didn't see any experiments showing that humans are reproductively isolated from chimps. Can you supply me with scientific evidence that humans and chimps are incapable of reproducing?

      The authors discuss the POSSIBILITY that pericentric inversions could lead to speciation but they present no evidence that this is the case in the great apes.

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    5. John Hawks is not an expert on chromosomal variations, human or otherwise.If you don't like the paper I cited which states that chromosomal rearrangement has the potential to create reproductive barriers, then I suggest you read this paper:

      Chromosome speciation in humans

      It clearly suggests that the chromosomal fusion was one of a number of steps leading to complete reproductive isolation. But the only way to absolutely confirm that humans and chimps are incapable of successfully interbreeding would be for someone to try it out. Would you be willing to donate some sperm to this end?

      Of course, if chimps and humans could interbreed then they would have to be recognized as being the same species.

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    6. Assuming that chimps and humans are incable of breeding, (biological species concept) then it is possible that the cumulated chromosomal rearrangements in the two lineages (including the fusion event) plays a role in that reproductive isolation.

      Why is this point so important to you? Who cares?

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    7. The question of reproductive isolation of chimps and humans has been addressed and, as we sit here today, is apparently somewhat controversial. Stephen J. Gould, in one of his essays opined that chimps and humans might be able to interbreed, although, like mules, the resulting hybrid would almost certainly be sterile. Others have stated that the chromosome difference among other issues, would prevent fertilization, or the production of a viable fetus.

      It should be noted that experiments were apparently conducted in the former Soviet Union, and possibly in Nazi Germany to artificially inseminate female chimps with male human sperm. These experiments were total failures. However, it is not clear that the failures were due to reproductive isolation as the techniques of artificial insemination were quite crude at the time. In particular, in-vitro fertilization techniques did not exist. However, as Gould argued in the same essay, the experiments are morally repulsive and it is doubtful that the experiments could be repeated today, using the modern insemination techniques. So unless some rogue scientist in a third world country performs the experiment, the controversy will probably remain.

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    8. Funny - I'm not seeing Joe Bozogomer's "evidence" from his "dissertation" regarding there being no junk DNA or whatever his assertion was...

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  7. I do note that Carl didn't answer the main point, that a fused chromosome could have happened to humans, such an event need not demonstrate common descent.

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    1. One way of addressing this issue would be to see whether the fused chromosome appears in Neanderthals. If it does, that would shoot down this argument.

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    2. Carl does answer this point! A chromosome fusion per se does not show common ancestry, but in the case of chromosome 2 there is strong evidence that it is a fusion of two ancestrally separate chromosomes. This evidence is described in Carl's post.

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  8. Sounds interesting, thanks for your reply.

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  9. I do note that Carl didn't answer the main point, that a fused chromosome could have happened to humans, such an event need not demonstrate common descent.

    No, Mr Merrill, that is not the main point. It is simply you and the other creationists being dishonest. It is the detailed DNA sequence similarity that is the evidence that demonstrates common descent, and Zimmer makes this clear:


    The rise of genome sequencing allowed them to test that hypothesis. They found that human chromosome two bears the hallmarks of an ancient chromosome fusion, with remnants of chromosome ends nestled at its core. In 2005, it became possible to test the hypothesis again, when a team of scientists sequenced the chimpanzee genome and could compare it to the human genome. The chimp genome team were able to match human chromosome two to two unfused chromosomes in the chimpanzee genome.

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    1. There is no real way of telling that the fusion event is 6 million years old or 6000 years old. Hence, it proves nothing.

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    2. There are plenty of ways of showing that the fusion event is much older than 6000 years.

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    3. I wasn't aware that sequences and mutations come with dates. I will be interested to see if the reconstructed genome of Homo hiedelbergensis has 48 or 46 chromosomes.

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    4. Atheistoclast:

      "There is no real way of proving that the fusion event is 6 million years old or 6000 years old. Hence, it proves nothing."

      Says the (supposed) grad student computer jockey who thinks he's more of en expert than people who have been studying this field for decades.

      Regardless of when it happened, it's further evidence of shared ancestry between humans, chimps, and gorillas. Are you really that dense, or are you deliberately arguing in bad faith?

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  10. But I meant the main point in the reply to Carl, that main point he did not answer. Certainly there is sequence similarity, which might (you know) be generally due to common function.

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    1. Seriously? That's your argument? So, how do you explain sequence similarity between non-coding regions?

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  11. "As for Intelligent Design Creationism, I'd be interested in debating anyone who wants to present scientific evidence for the existence of an intelligent designer."

    That's a little disingenuous, though, you wouldn't ask for scientific evidence of Henry Ford, now, would you? Science's province is natural processes, so if an intelligent designer were a natural process, it would be in the domain of science.

    That is not to say that there are no scientific aspects to design questions, the SETI search comes to mindd. I think Behe's book sums up the best ID argument, and I don't believe you have exactly refuted him here.

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    1. That's a little disingenuous, though, you wouldn't ask for scientific evidence of Henry Ford, now, would you? Science's province is natural processes, so if an intelligent designer were a natural process, it would be in the domain of science.

      The reason we don't ask for scientific evidence of Henry Ford is that there is more than sufficient to establish his existence as fact under Gould's definition. The same cannot be said of any putative Intelligent Designer so it is perfectly reasonable to ask any proponent of such a claim to meet their burden of proof if they want to persuade us that the claim has merit. If any such extraterrestrial designer exists then, yes, it would fall within the domain of science.

      The existence of design in the universe is not in doubt. We do it. And if the universe is so arranged as to allow designers such as ourselves to exist then it is reasonable to consider the possibility that there are others elsewhere. If it can happen once, it can happen again. The question is, have any of those others paid a visit to our neck of the galaxy at some time in the past Another question, of course, is who designed them and is it designing turtles all the way down?

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    2. I think Behe's book sums up the best ID argument, and I don't believe you have exactly refuted him here.

      Which book?

      Both of Behe's books make the same claim; namely that there are biological bits that can't possibly be produced by any known mechanism of evolution. Therefore, god did it.

      Many of us have shown that there are quite reasonable evolutionary pathways to the things that Behe claims are out of bounds. His argument fails.

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    3. I think Behe's book sums up the best ID argument

      Behe's first book is very strong on propaganda - one of the best books ever as an example how to write propaganda - but seriously deficient in arguments. Behe immediately gets folded on his own definition of irreducible complexity.

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    4. > Ian: If any such extraterrestrial designer exists then, yes, it would fall within the domain of science.

      But it would not be essentially a scientific question, the scientific part would be like the ID area, is this object (or radio wave) have a likely natural cause?

      > Another question, of course, is who designed them and is it designing turtles all the way down?

      Good question! I'm rather fond of turtles.

      > Heleen: Behe immediately gets folded on his own definition of irreducible complexity.

      But see here, where Behe gives a more practical definition.

      > Prof. Moran: Many of us have shown that there are quite reasonable evolutionary pathways to the things that Behe claims are out of bounds.

      Yet the argument in Edge of Evolution does not depend at its base on evolutionary mechanisms. Behe first examines the rate at which certain mutation combinations occur, this then results in a rate for a double-CCC event, as he calls it, which is the base for his argument on the rate of new protein-protein interactions.

      So proposing a mechanism that gets around this would only show that evolution should occur here at a faster rate than it actually does.

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    5. Behe's argument is correct in one important respect. If several mutations have to happen simultaneously for something to evolve then there's a limit (double-CCC) to what evolution can accomplish. All biologists who have thought seriously about the problem wiil agree with Behe on this point.

      Where we disagree with Behe is whether observed evolutionary events—such as protein-protein interactions—require simultaneous mutations and whether each mutation in a pathway has to have a positive effect on fitness. The scientifc evidence of protein evolution shows clearly that his special assumptions are wrong. Many of the mutations that evevtually contribute to improved fitness are neutral on their own and some are even slighly deleterious. They can arise and be fixed independently, not simultaneously. Lenski's work on the E. coli long-term evolution experiment provides a nice illustration of why Behe's assumptions are wrong.

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    6. Thanks for your reply, Prof. Moran.

      > Prof. Moran: Many of the mutations that eventually contribute to improved fitness are neutral on their own and some are even slightly deleterious.

      Yet Behe is aware of this: "... let's suppose that of the five or six changes that have to happen to a protein to make a new binding site, a third of them are neutral." (p. 134)

      So I'm not sure where exactly the error is here.

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  12. The idea with the chromosome fusion argument, at least to me, was always that it had the potential to falsify common descend between H. Sapiens and the other great apes but didn't. Did I mistunderstand something?

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    1. On the contrary, if the fusion had not been found, the notion that chimps and humans share a common ancestor would be in serious trouble.

      http://www.youtube.com/watch?v=zi8FfMBYCkk

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    2. But that's exactly what Rumraket just said.

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  13. I see Cornelius Hunter has weighed in on the chromosome fusion debate over on Darwin's God

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